Category Archives: Human oral

Human microbiome digest, August 25, 2014

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Oral microbiome in the settings of periodontitis, smoking and antibiotic resistance, respiratory microbiome in Cystic Fibrosis, a decade of molecular papers on vaginal microbiome, and gut bacteria protecting against food allergies.

Oral microbiome

* Microbial Signature Profiles of Periodontally Healthy and Diseased Patients – Talita Gomes Baêta Lourenço – Journal of Clinical Periodontology

“Subgingival biofilm was obtained from patients with periodontal health (27), gingivitis (11), chronic periodontitis (35) and aggressive periodontitis (24), and analyzed for the presence of >250 species/phylotypes using HOMIM. “

Smoking decreases structural and functional resilience in the subgingival ecosystem – Vinayak Joshi – Journal of Clinical Periodontology

“16S cloning and sequencing was used for bacterial identification and multiplexed bead-based flow cytometry was used to quantify the levels of 27 immune mediators.”

Extended-spectrum beta-lactamase-producing bacteria are not detected in supragingival plaque samples from human fecal carriers of ESBL-producing Enterobacteriaceae – Arne Søraas – Journal of Oral Microbiology

“No ESBL-producing bacteria or ESBL genes were detected using culture-based and molecular methods. “

Clonality of bacterial consortia in root canals and subjacent gingival crevices – Nipuna B. Parahitiyawa – Journal of Investigative and Clinical Dentistry

“The four niches studied yielded 186 clones representing 54 phylotypes. Clone library comparisons using LIBSHUFF software indicated that each niche was inhabited by a unique flora. “

Respiratory microbiome

* Antimicrobial resistance in the respiratory microbiota of people with cystic fibrosis –
Laura J Sherrard – The Lancet

“Strategies to manage antimicrobial resistance consist of new antibiotics or localised delivery of antimicrobial agents, iron sequestration, inhibition of quorum-sensing, and resistome analysis.”

Evidence that Intraspecific Trait Variation among Nasal Bacteria Shapes the Distribution of Staphylococcus aureus – Ben Libberton – Infection and Immunity

“We characterized S. aureus growth inhibition by the culturable bacterial aerobe consortia of 60 nasal microbiomes, and this revealed intraspecific variation in growth inhibition and that inhibitory isolates clustered within communities that were culture negative for S. aureus. “

Gary Huffnagle: rewriting the rules on the lung microbiome – David Holmes – The Lancet

“The ideas being generated by Huffnagle at the moment are all about the lung microbiome and its role in the pathogenesis of everything from chronic obstructive pulmonary disease (COPD) to asthma, and they’re starting to make waves.”

Vaginal microbiome

* The Vaginal Microbiota: What Have We Learned after a Decade of Molecular Characterization? – Janneke H. H. M. van de Wijgert – PLOS ONE

“We conducted a systematic review of the Medline database … to determine if consistent molecular vaginal microbiota (VMB) composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions.”

Gut microbiome

Modelling the Emergent Dynamics and Major Metabolites of the Human Colonic Microbiota – Helen Kettle – Environmental Microbiology

“We present here a first attempt at modelling microbial dynamics in the human colon incorporating both uncertainty and adaptation. “

Animal models of human microbiome

Commensal bacteria protect against food allergen sensitization – Andrew T. Stefka – PNAS USA

“By selectively colonizing gnotobiotic mice, we demonstrate that the allergy-protective capacity is conferred by a Clostridia-containing microbiota. “

Pregnancy and Birth

Researcher Granted $1 Million to Study Deadly Bacteria Passed to Babies From 25 Percent of Mothers – Infection Control Today

“Narayana Sthanam, PhD, professor of structural biology in the Department of Optometry, has been awarded a four-year, $1 million R01 grant from the National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health, to further Group B Streptococcus research.”

Microbiome News

* Satire: Study Reveals Microbiome To Be Master-Controller Of All Humanity – The Allium

“Science has already found out that your microbiome at birth decides your taste in clothes and music, whether you are going to be great footballer like David Beckham or a great political leader like Sarah Palin.”

9 questions you were too grossed out to ask about the bacteria living on you – Susannah Locke – Vox

“What researchers have discovered is that our bodies are essentially complex ecosystems of tiny living things. “

Interview with Prof. Yolanda Sanz, project coordinator of My New Gut – Kristina Campbell – Gut Microbiota For Health

“Professor Yolanda Sanz has been appointed MyNewGut’s project coordinator and leads the project’s human intervention trials on the gut microbiome’s ability to metaolise (sic) nutrients and influence energy balance. “

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Human microbiome digest, August 19, 2014

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Lots of oral and gut microbiome papers today – Alzheimer’s, probiotics, chemotherapy and radiation.

Oral microbiome

Review: The Microbiome and Disease: Reviewing the Links between the Oral Microbiome, Aging, and Alzheimer’s Disease – Deborah K. Shoemark – Journal of Alzheimer’s Disease

“Evidence linking oral bacteria to Alzheimer’s disease (AD) is discussed in the context of aging, drawing together data from epidemiological, experimental, genetic, and environmental studies. “

* Human oral viruses are personal, persistent and gender-consistent – Shira R Abeles – ISME Journal

“To improve our understanding of the DNA viruses that inhabit the human oral cavity, we examined saliva from a cohort of eight unrelated subjects over a 60-day period. “

* Predictive modeling of gingivitis severity and susceptibility via oral microbiota – Shi Huang – ISME Journal

“In diseased plaque microbiota, 27 bacterial genera changed in relative abundance and functional genes including 33 flagellar biosynthesis-related groups were enriched.”

Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients – Yan Li – ISME Journal

“Here, we examined the phylogenetic and functional gene differences between periodontal and healthy individuals using MiSeq sequencing of 16S rRNA gene amplicons and a specific functional gene array”

Perspective: Fungal-bacterial interactions and their relevance to oral health: linking the clinic and the bench – Patricia I. Diaz – Frontiers in Cellular and Infection Microbiology

“We highlight the need to conduct longitudinal clinical studies to simultaneously characterize the bacterial and fungal components of the human oral microbiome in health and during disease progression.”

Effect of an oxygenating agent on oral bacteria in vitro and on dental plaque composition in healthy young adults – Mercedes Fernandez y Mostajo – Frontiers in Cellular and Infection Microbiology

“During the experiment individuals used AX mouthwash twice daily in absence of other oral hygiene measures. The microbiological composition of plaque was assessed by 16S rRNA gene amplicon sequencing.”

* Review: Advancements toward a systems level understanding of the human oral microbiome
Jeffrey S. McLean – Frontiers in Cellular and Infection Microbiology

“This review will discuss some of the recent insights into the oral microbiome at a fundamental level, existing knowledge gaps, as well as challenges that have surfaced and the approaches to address them.”

Gut microbiome

* Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes – Meiling Zhang – PNAS USA

“Here we demonstrate that two human gut commensal Bacteroides are equipped with unique enzymes that allow degradation of xylan, a common hemicellulose in human diets.”

Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol – Christian Milani – FEMS Microbiology Ecology

“Here, we define the internal transcribed spacer (ITS) sequences of all currently known Bifidobacterium taxa, providing a Bifidobacterium-specific primer pair that targets a hyper-variable region within the ITS suitable for precise taxonomic identification of all 48 so far recognized members of the Bifidobacterium genus.”

* Multi-omics analysis of Inflammatory Bowel Diseases – Hu Huang – Immunology Letters

“There is strong evidence of interactions between host genotype, environment, and gut microbiome profile in IBD.”

The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei – Michael T. Leonard – Frontiers in Microbiology

“Here metagenomic sequencing using the Pacific Biosciences platform allowed for rapid identification of bacterial GATC methylation status of a bacterial species in human stool samples. “

Perspective: Imposition of encapsulated non-indigenous probiotics into intestine may disturb human core microbiome – Abolfazl Barzegari – Frontiers in Microbiology

“..we envision that multi-probiotic therapy and holistic personalized microbiome supplements may be scientifically justified and valued in individualized probiotic designs and even targeted therapy of life-threatening diseases such as cancers in the future. “

Editorial: gut microbiota and chemotherapy- or radiation-induced gastrointestinal mucositis – M. R. Ferreira and H. J. N. Andreyev – Alimentary Pharmacology & Therapeutics

“Studies in those undergoing cancer therapy will lead to a new era in the treatment and prevention of the currently dreadful GI toxicity suffered by so many patients, and what we learn will almost certainly bring important insights to many other GI disorders.”

Respiratory microbiome

Cell-associated bacteria in the human lung microbiome – Robert P Dickson – Microbiome

“We present a novel methodological and analytical approach to the localization of lung microbiota and show that the prominent members of the lung microbiome are cell-associated, potentially via biofilms, cell adhesion, or intracellularity.”

Vaginal microbiome

A Systems Biology Approach Investigating the Effect of Probiotics on the Vaginal Microbiome and Host Responses in a Double Blind, Placebo-Controlled Clinical Trial of Post-Menopausal Women – Jordan E. Bisanz – PLOS ONE

“Analysis using 16S rRNA sequencing and metabolomics profiling revealed that the relative abundance of Lactobacillus was increased following probiotic administration as compared to placebo, which was weakly associated with an increase in lactate levels. “

Lactobacillus-dominated cervicovaginal microbiota associated with reduced HIV/STI prevalence and genital HIV viral load in African women – Hanneke Borgdorff – ISME Journal

“In this study, cervical samples of 174 Rwandan female sex workers were analyzed cross-sectionally using a phylogenetic microarray. “

* also tweeted by @MicrobiomDigest (yup, that’s me).

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Microbiome digest, August 15, 2014

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Today we got donkey, goat, and camel milk, deodorants, kitten microbiomes, and coffee as a new mouth rinse.

Pregnancy and birth

Gut microbiota in preterm infants with gross blood in stools: A prospective, controlled study – Mohamed Ben Said – Early Human Development

“Each case was paired with two controls who were hospitalized in the same unit and were matched for gestational age and birth weight. The diversity of the gut microbiota was analyzed using 16S rRNA gene PCR and temporal temperature gel electrophoresis. “

Human oral microbiome

Antibacterial effect of coffee: calcium concentration in a culture containing teeth/biofilm exposed to Coffea Canephora aqueous extract – N. Meckelburg – Letters in Applied Microbiology

“This study revealed an inhibitory action of Coffea canephora against dental biofilm. This coffee species caused bacterial lysis and consequent release of calcium into the medium.”

Human gut microbiome

Review: Exploring gut microbes in Human health and disease: pushing the envelope
Jun Sun, Eugene B. Chang – Genes & Diseases

“In this review and commentary, we highlight recent progress in our understanding of the intestinal microbiome in the context of health and diseases, focusing on mechanistic concepts that underlie the complex relationships between host and microbes.”

Review: Emergence of fecal microbiota transplantation as an approach to repair disrupted microbial gut ecology – Alexander Khoruts, Alexa R. Weingarden – Immunology Letters

“Mechanistic understanding will be required in development of next generation microbiota therapeutics, which may include FMT or defined microbial consortia.”

Gut Bacteria May Play a Role in Autism – Melinda Wenner Moyer – Scientific American

“One open question is whether these microbial differences drive the development of the condition or are instead a consequence of it. “

Skin microbiome

Deodorants and antiperspirants affect the axillary bacterial community – Chris Callewaert — Archives of Dermatological Research

“The effect of deodorants and antiperspirants on the axillary bacterial community was examined on nine healthy subjects, who were restrained from using deodorant/antiperspirant for 1 month. Denaturing gradient gel electrophoresis was used to investigate the individual microbial dynamics.”

Goat and Ass Milk microbiome

Analysis of raw goat milk microbiota: Impact of stage of lactation and lysozyme on microbial diversity – Elizabeth A. McInnis – Food Microbiology

“Milk from transgenic goats containing lysozyme had a similar microbiota over time.”

Fasscinating stuff: Cleopatra took daily baths in assmilk to keep her skin wrinklefree. Maybe lactic acid bacteria were her secret?  Biotyping of cultivable lactic acid bacteria isolated from donkey milk – D. Carminati – Letters in Applied Microbiology

“The large amounts of antimicrobial components and defence factors present in donkey’s milk provide protection from microbial infections and distinguish donkey’s milk from the milks of other mammals”

The Kitten Microbiome Project

“Keeping track of the cutest, fluffiest microbiome project around”

Insect microbiome

Microbial impacts on insect evolutionary diversification: From patterns to mechanisms
Fabrice Vavre, Natacha Kremer – Current Opinion in Insect Science

“Symbiosis can favor rapid shifts in host phenotypic traits, particularly through the contribution of symbionts to the host’s physiology.”

How resident microbes modulate ecologically-important traits of insects
Kerry M. Oliver, Adam J. Martinez – Current Opinion in Insect Science

“In addition to their better-known roles in nutrient provisioning and degrading plant polymers, there is emerging evidence that microorganisms also aid herbivores in countering plant defenses. “

Metabolomics

Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking – Kalai Vanii Jayaseelan and Christoph Steinbeck – BMC Bioinformatics

“In this study, we investigated whether additional existing knowledge, such as the fact that the unknown compound is a natural product, can be used to improve the ranking of the correct structure in the result list after the structure elucidation process.”

Phages and viruses

Bacteriophage as effective decolonising agent for elimination of MRSA from anterior nares of BALB/c mice – Sanjay Chhibber – BMC Microbiology

“Phage MR-10, given along with mupirocin showed an additive effect and the combination was able to effectively eradicate the colonising MRSA population from the nares of mice by day 5.”

Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target – Sabin Mulepati, Annie Héroux, Scott Bailey – Science

“The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. “

Bik’s Picks – weekend edition

15 Real-Life Scientists Share Their Favorite Science Fiction Books, Movies – Jacqueline Howard – Huffington Post

“There’s a big difference between science and science fiction, but there’s abundant evidence to suggest that sci-fi books and movies can spark a lifelong interest in science.”

After donkey and goat milk, this one was only appropriate: A Nice Tall Glass of Camel’s Milk – Olga Khazan – The Atlantic

“An oasis in the dromedary-dairy desert?”

Male Mathematicians Agree That Fields Medal Gender Balance Is Now OK – The Allium

“Now that a woman has won the fields medal, there is true and genuine equality and there is no need to worry any more about it.”

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Human microbiome, August 14, 2014

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Culturing TM7, antibiotics early in life and obesity, preterm labor, breast milk, two articles by Carl Zimmer and one by Jop de Vrieze.

Pregnancy and Birth

Science has a special this week on Parenting, with a couple of relevant papers:

Preterm labor: One syndrome, many causes – Roberto Romero, Sudhansu K. Dey, Susan J. Fisher – Science

“We summarize the current understanding of the mechanisms of disease implicated in this condition and review advances relevant to intra-amniotic infection, decidual senescence, and breakdown of maternal-fetal tolerance.”

Nature’s first functional food – Trisha Gura – Science

“Building upon a century-old study that first indicated that milk nourished certain bacteria in infants, the new work has characterized the complexity of breast milk carbohydrates called oligosaccharides, or HMOs, that particularly nourish one species of beneficial bacteria.”

The taste of things to come – Emily Underwood – Science

“Indeed, studies in human infants and animals suggest that we may start to learn and love different flavors as early as in the womb.”

Human oral microbiome

Axenic Culture of a Candidate Division TM7 Bacterium from the Human Oral Cavity and Biofilm Interactions with Other Oral Bacteria – Valeria Soro – Applied and Environmental Microbiology

“Successive rounds of enrichment in laboratory media led to the isolation of a pure culture of one of these candidate division TM7 phylotypes.”

Human gut microbiome

Review: Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics – Rachel N. Carmody and Peter J. Turnbaugh – Journal of Clinical Investigation

“Here, we integrate results from classic and current studies of the direct and indirect impacts of the gut microbiome on the metabolism of therapeutic drugs and diet-derived bioactive compounds. “

Taking the Yuck Out of Microbiome Medicine – Carl Zimmer – National Geographic

“I can still remember the shock I felt when I heard about fecal microbiota transplants for the first time. It is not the sort of thing you forget.”

Our Microbiome May Be Looking Out for Itself – Carl Zimmer – New York Times

“But in the journal Bioessays, a team of scientists has raised a creepier possibility. Perhaps our menagerie of germs is also influencing our behavior in order to advance its own evolutionary success — giving us cravings for certain foods, for example.”

Animal models of microbiome research

Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences – Laura M. Cox – Cell

Press coverage: Taking antibiotics early in life leaves mice prone to obesity – Jop de Vrieze

“A new study of mice shows that interrupting the development of gut microbial populations with low doses of antibiotics early in life disturbs their metabolism and boosts the risk of obesity later on.”

The Gut Microbiota and Developmental Programming of the Testis in Mice – Maha Al-Asmakh – PLOS ONE

“Interestingly, exposure of GF mice to Clostridium Tyrobutyricum (CBUT), which secrete high levels of butyrate, restored the integrity of the BTB and normalized the levels of cell adhesion proteins. “

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Human microbiome, August 12, 2014

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Oral microbiome in Aboriginals, gut microbiome and probiotics.

Human oral microbiome

Age-dependent changes in Porphyromonas gingivalis and Prevotella species/phylotypes in healthy gingiva and inflamed/diseased sub-gingival sites – Mangala A. Nadkarni – Clinical Oral Investigations

“The aims of the present study were to establish the age-dependent relationship between sub-gingival profiles of 22 Prevotella species/phylotypes in children, adolescents and adults from an isolated Aboriginal community and, further, to use this information to identify Prevotella species that could serve as microbial risk indicators.”

The effect of propidium monoazide treatment on the measured bacterial composition of clinical samples after the use of a mouthwash – R. A. M. Exterkate – Clinical Oral Investigations

“Propidium monoazide (PMA) has been used to overcome this problem, by preventing the amplification of DNA from membrane-damaged cells. The aim of this study was to evaluate the use of PMA when measuring compositional shifts in clinical samples after mouthwash use.”

Human gut microbiome

Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms – Joe Alcock – BioEssays

“We review several potential mechanisms for microbial control over eating behavior including microbial influence on reward and satiety pathways, production of toxins that alter mood, changes to receptors including taste receptors, and hijacking of the vagus nerve, the neural axis between the gut and the brain”

Influence of the microbiota on vaccine effectiveness – Yanet Valdez – Trends in Immunology

“Recent findings suggest novel complex mechanisms by which the microbiome impacts immune cell development and differentiation.”

Current Status and Prospects of Intestinal Microbiome Studies – Dong Soo Han – Intest Res

“Evidences have implicated gut microbes in the development of IBD, but no causative microorganisms have been identified.”

Synbiotic Lactobacillus acidophilus NCFM and cellobiose does not affect human gut bacterial diversity but increases abundance of lactobacilli, bifidobacteria and branched-chain fatty acids: a randomized, double-blinded cross-over trial – Gabriella C. van Zanten – FEMS Microbiology Ecology

“Furthermore, 454 tag encoded amplicon pyrosequencing was used to monitor the effect of synbiotic on the composition of the microbiota. “

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Microbiome digest, August 7, 2014

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Microbiome and caries, colorectal cancer, and inflammatory bowel diseases. Microbiomes of fish, dogs, and mosses, microscopic life in an asphalt lake, and the Picks.

Human mouth microbiome

Identification of the Microbiota in Carious Dentin Lesions Using 16S rRNA Gene Sequencing – Junko Obata – PLOS ONE

“In the present study, the bacterial communities in the carious dentin of Japanese subjects were analyzed comprehensively with molecular approaches using the 16S rRNA gene.”

Human gut microbiome

The Human Gut Microbiome as a Screening Tool for Colorectal Cancer – Joseph P. Zackular, Mary A.M. Rogers, Mack T. Ruffin IV, and Patrick D. Schloss – Cancer Prevention Research

“Analysis of the gut microbiome from stool samples revealed both an enrichment and depletion of several bacterial populations associated with adenomas and carcinomas.”

Manipulation of Microbiome, a Promising Therapy for Inflammatory Bowel Diseases – Dapeng Jin, Hongyu Zhang, and Jun Sun – Clinical & Cellular Immunology

“In this review, we summarize the current knowledge of how changes in microbiota may affect the pathogenesis of IBD. “

A perspective on the complexity of dietary fiber structures and their potential effect on the gut microbiota – Bruce R. Hamaker, Yunus E. Tuncil – Journal of Molecular Biology

“the article encourages the building of a framework of information to manipulate the colon microbiota in a predicted way for improved health”

 

Human microbiome after death

Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans – Ismail Can – Journal of Microbiological Methods

“We compared the effectiveness of two methods by amplifying the 16S rRNA genes and sequencing the amplicons from four cadavers”

Animal models of human microbiome

Disturbance of the gut microbiota in early-life selectively affects visceral pain in adulthood without impacting cognitive or anxiety-related behaviors in male rats
S.M. O’Mahony – Neuroscience

“Neonatal antibiotic treatment leads to an increase in visceral sensitivity in adulthood in rats.”

Dog microbiome

The Unculturables: targeted isolation of bacterial species associated with canine periodontal health or disease from dental plaque – Ian J Davis, Christopher Bull, Alexander Horsfall, Ian Morley and Stephen Harris – BMC Microbiology

“Using a quantitative polymerase chain reaction (qPCR) directed approach a range of microbiological media were screened and optimized to enrich for previously uncultivated target species. A systematic screening methodology was then employed to isolate the species of interest. ‘

Fish microbiome

Characterization of Microbiota Composition and Presence of Selected Antibiotic Resistance Genes in Carriage Water of Ornamental Fish – Lenka Gerzova – PLOS ONE

“In this study we therefore characterized the prevalence of selected antibiotic resistance genes in the microbiota found in the carriage water of ornamental fish originating from 3 different continents.”

Insect microbiome

The mosquito microbiota influences vector competence for human pathogens – Nathan J Dennison, Natapong Jupatanakul, George Dimopoulos – Current Opinion in Insect Science

“Understanding the interaction between the vector, its microbiota and transmitted pathogens will provide novel opportunities to limit disease transmission.”

Plant microbiome

Bacterial-biota dynamics of eight bryophyte species from different ecosystems
Faisal Hammad Mekky Koua – Saudi Journal of Biological Sciences

“..we utilized the 16S rRNA gene PCR-DGGE and subsequent phylogenetic analyses to investigate the bacterial community of eight bryophyte species collected from three distinct ecosystems from western Japan.”

Soil and water microbiome

Two Neumann U students discover new types of viruses – CatholicPhilly.com

“They collected arthrobacter (a bacteria present in soil) from under trees and near lakes, found and filtered out the phages that were present, and then studied phage anatomy and life cycles.”

Water droplets in oil are microhabitats for microbial life – Rainer U. Meckenstock – Science

“In Pitch Lake, Trinidad and Tobago—the world’s largest asphalt lake—we found that microorganisms are metabolically active in minuscule water droplets (1 to 3 microliters) entrapped in oil. “

Microbiome of the built environment

Halophilic Microorganisms Are Responsible for the Rosy Discolouration of Saline Environments in Three Historical Buildings with Mural Paintings – Jörg D. Ettenauer – PLOS ONE

“In order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolouration of mural paintings in three Austrian historical buildings using a combination of culture-dependent and -independent techniques as well as microscopic techniques.”

Metagenomics

High-resolution metagenomics – Eran Mick & Rotem Sorek – Nature Biotechnology

In this issue, Nielsen et al. present a powerful method for interpreting metagenomic data at the level of individual genomes without relying on reference sequences of cultured isolates, which can be generated for only a small fraction of microbial life.

Microbes in the News

The Quantified Microbiome Self – Carl Zimmer – National Geographic

“But as I read the journal Genome Biology today, I decided that someday I might surrender to the Quantified Self movement. I’ll just have to wait till I can track my trillions of microbes from one day to the next.”

Science and Career

Ph.D.’s, come out of the closet! – Lina Nilsson – Science

“If you promise not to tell Fisher’s Ph.D. adviser (or mine), I’ll let you in on this well-hidden truth: Fisher isn’t planning to pursue an academic career.”

Bik’s Picks

Stress during pregnancy can be passed down through generations, rat study shows – Science Daily

“Scientists investigating pregnancies in four generations of rats show that inherited epigenetic effects of stress could affect pregnancies for generations.”

This Is Your Brain on Fish – James Hamblin – The Atlantic

“Thicker, stronger, and more resilient. Once a week is all it takes, new research says.”

10 Great Novels That Will Make You More Passionate About Science – Charlie Jane Anders – io9

“A lot of the best science fiction features scientists who solve problems and make breakthroughs.”

Scientist looking forward to weekend of binge-experimenting – The Allium

“Imperial college Scientist Dr. Lou Pole announced earlier today that he was going to spend the entirety of this weekend binge-experimenting.”

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Human microbiome digest, August 5, 2014

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Lots of microbiome papers today, so I will split it up into three posts. Here you will find papers on human gut, respiratory, oral, and vaginal microbiomes, as well as animal models.

Pregnancy and Birth

Prevalence and Clinical Significance of Sterile Intra-amniotic Inflammation in Patients with Preterm Labor and Intact Membranes – Roberto Romero – American Journal of Reproductive Immunology

“The purpose of this study was to (i) determine the prevalence and clinical significance of sterile intra-amniotic inflammation and (ii) examine the relationship between amniotic fluid (AF) concentrations of high mobility group box-1 (HMGB1) and the interval from amniocentesis to delivery in patients with sterile intra-amniotic inflammation.”

A Holobiont Birth Narrative: The Epigenetic Transmission of the Human Microbiome –
Scott F. Gilbert – Frontiers in Genetics

“Birth is nothing less than the passage from one set of symbiotic relationships to another.”

Fecal Short Chain Fatty Acids of Very Low Birth Weight Preterm Infants Fed Expressed Breast Milk or Formula – Pourcyrous, M.; Nolan, V.G.; Goodwin, A.; Davis, S.L.; Buddington, R.K. – Journal of Pediatric Gastroenterology & Nutrition

“ Ion chromatography was used to measure fecal SCFAs (acetate, formate, propionate, butyrate, and isobutyrate), lactate, and chloride in fresh stool samples collected from 32 preterm infants”

Human mouth microbiome

Microbial community in persistent apical periodontitis: a 16S rRNA gene clone library analysis – M. N. Zakaria – International Endodontic Journal

“DNA was directly extracted from each sample and the microbial composition was comprehensively analyzed using clone library analysis of the 16S rRNA gene”

 Respiratory microbiome

A large genomic island allows Neisseria meningitidis to utilize propionic acid, with implications for colonization of the human nasopharynx – Maria Chiara E. Catenazzi, Helen Jones, Iain Wallace, Jacqueline Clifton, James P. J. Chong, Matthew A. Jackson, Sandy Macdonald, James Edwards andJames W. B. Moir – Molecular Microbiology

“Data from classical microbiological and sequence-based microbiome studies provide several lines of supporting evidence that N. meningitidis colonization is correlated with propionic acid generating bacteria, with a strong correlation between prp-containing Neisseria and propionic acid generating bacteria from the genus Porphyromonas, and that this may explain adolescent/adult colonization by N. meningitidis.”

Analysis of Culture-Dependent vs. Culture-Independent Techniques for the Identification of Bacteria in Clinically-Obtained Bronchoalveolar Lavage Fluid – Robert P. Dickson – Journal of Clinical Microbiology

“We analyzed forty six clinically-obtained bronchoalveolar lavage (BAL) specimens from symptomatic and asymptomatic lung transplant recipients both by culture (using a clinical microbiology laboratory protocol) and by bacterial 16S rRNA gene pyrosequencing. “

Vaginal microbiome

Differences in vaginal microbiome in African American women versus women of European ancestry – Jennifer M. Fettweis – Microbiology

“we performed 16S rRNA gene survey to compare the microbiomes of vaginal samples from 1,268 African American women and 416 women of European ancestry. Our results confirmed significant differences in the vaginal microbiomes of the two groups and identified several taxa relevant to these differences.”

Human gut microbiome

Unraveling the mechanisms underlying associations between the microbiome and gastrointestinal malignancies – Tiffany L. Weir – Translational Gastrointestinal Cancer

“While many reviews have focused on research identifying microbial signatures associated with malignancies, including changes in diversity or evenness of GI microbial communities and depletion or overrepresentation of particular bacterial groups; this comprehensive review emphasizes research that explores the cause rather than effects of microbe-malignancy relationships.”

Animal models of human microbiome

Transfer of gut microbiota from lean and obese mice to antibiotic-treated mice – Merete Ellekilde, Ellika Selfjord, Christian S. Larsen, Maja Jakesevic, Ida Rune, Britt Tranberg, Finn K. Vogensen, Dennis S. Nielsen, Martin I. Bahl, Tine R. Licht, Axel K. Hansen & Camilla H. F. Hansen – Nature Scientific Reports

“To date, most studies of gut microbiota transfer are performed in germ-free mice. In the studies presented, it was tested whether an antibiotic treatment approach could be used instead. “

Postnatal Prebiotic Fiber Intake in Offspring Exposed to Gestational Protein Restriction Has Sex-Specific Effects on Insulin Resistance and Intestinal Permeability in Rats – Megan C. Hallam and Raylene A. Reimer – Journal of Nutrition

“At 24 wk of age, glucose tolerance, body composition, satiety hormones, gut microbiota, and markers of intestinal permeability were measured in the offspring. “

A polyphenol-rich cranberry extract protects from diet-induced obesity, insulin resistance and intestinal inflammation in association with increased Akkermansia spp. population in the gut microbiota of mice – Fernando F Anhê – Gut

“CE exerts beneficial metabolic effects through improving HFHS diet-induced features of the metabolic syndrome, which is associated with a proportional increase in Akkermansia spp. population.”

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Human microbiome, July 28

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Oral microbes balancing their budgets, bacteria see blue, why Obama likes to fist bump, Gardnerella, and oxygen gradients in the gut.

Oral microbiome

Bioinformatic investigation of the cost management strategies of five oral microbes – Keith J. Cross – Molecular Oral Microbiology

“For Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia, and Streptococcus sanguinis, the outer membrane/extracellular proteins are made up of a much larger percentage of lower average mass amino acids whereas cytoplasmic proteins are made up of a larger proportion of higher average mass amino acid residues.”

Code blue: Acinetobacter baumannii, a nosocomial pathogen with a role in the oral cavity – Ashley M. Richards – Molecular Oral Microbiology

“A. baumannii can sense blue light through a blue-light sensing using flavin (BLUF) domain protein, BlsA. The resulting conformational change in BlsA leads to changes in gene expression, including virulence genes.”

Skin microbiome

Study: Fist bumps are less germy than handshakes – Kim Painter – USA Today

“Whitworth and a colleague systematically tested the three greetings for a study published Monday in the American Journal of Infection Control.” (article not available yet – MD).

Vaginal microbiome

Gardnerella vaginalis Outcompetes 29 Other Bacterial Species Isolated From Patients With Bacterial Vaginosis, Using in an In Vitro Biofilm Formation Model – Patrícia Alvesa – Journal of Infectious Diseases

“Here, we isolated 30 BV-associated species and characterized their virulence, using an in vitro biofilm formation model. “

Long-term Effect of Depot Medroxyprogesterone Acetate on Vaginal Microbiota, Epithelial Thickness and HIV Target Cells – Caroline M. Mitchell – Journal of Infectious Diseases

“Vaginal microbiota of women using DMPA for up to 2 years were cultured. Mucosal immune cell populations were measured by immunohistological staining.”

Gut microbiome

Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota in Humans and Mice – L. Albenberg – Gastroenterology

“In humans, 16S rRNA gene analyses revealed an increased proportion of oxygen-tolerant organisms of the Proteobacteria and Actinobacteria phyla associated with the rectal mucosa, compared with the feces, indicating an effect of oxygenation on the microbiota. “

Patients with cystic fibrosis have a high carriage rate of non-toxigenic Clostridium difficile – M. P. Bauer – Clinical Microbiology and Infection

“In this case-control study, we found more carriers among CF patients than controls (47% versus 11%), but most strains carried by CF patients were non-toxigenic (77% versus 17%). “

Animal models of human microbiome and disease

Obese-type Gut Microbiota Induce Neurobehavioral Changes in the Absence of Obesity
Annadora J. Bruce-Keller – Biological Phychiatry

“Sequencing-based phylogenetic analysis confirmed the presence of distinct core microbiota between groups, with alterations in α- and β-diversity, modulation in taxonomic distribution, and statistically significant alterations to metabolically active taxa. “

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Microbiome Digest, July 25

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A year worth of oral/stool samples shows relative stability, antibiotics and preterm infants, reagent contamination, and 42. Have a great weekend!

 

Oral and gut microbiome

Screen Shot 2014-07-25 at 9.45.01 PMHost lifestyle affects human microbiota on daily timescales – Lawrence A David – Genome Biology

“Here, we link over 10,000 longitudinal measurements of human wellness and action to the daily gut and salivary microbiota dynamics of two individuals over the course of one year. These time series show overall microbial communities to be stable for months. However, rare events in each subjects’ life rapidly and broadly impacted microbiota dynamics. “

Pregnancy and Birth

Screen Shot 2014-07-25 at 9.44.20 PMThe impact of postnatal antibiotics on the preterm intestinal microbiome – Majd Dardas – Pediatric Research

“Rectal (fecal) swabs were collected at 10 and 30 d and analyzed by 16S rRNA pyrosequencing. At both time points, we examined the rectal microbiome from infants who received only 2 d of antibiotics and those who received at least 7 d of antibiotics.”

Techniques

Screen Shot 2014-07-25 at 9.45.50 PMReagent contamination can critically impact sequence-based microbiome analyses – Susannah Salter – BioRxiv (preprint)

“In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. “

Dengue

Speaking about “matter of timing”, seems like this paper came out a bit too late.
Screen Shot 2014-07-25 at 9.46.14 PMDengue and the World Football Cup: A Matter of Timing – Christovam Barcellos, Rachel Lowe – PLOS Neglected Tropical Diseases

“We provide a nationwide risk map, averaging June dengue incidence rates for 2001–2012. The areas along the Amazonian rivers and in the inner portions of southernmost states are actually low-risk areas, while elevated dengue risk is found in the central Brazilian plateau.”

Infection and host response

Don’t forget your towel! Even the issue number, 1004201, contains the “The Answer to the Ultimate Question of Life, the Universe, and Everything”. Perfection.
Screen Shot 2014-07-25 at 9.46.22 PMMicrobial Egress: A Hitchhiker’s Guide to Freedom – Ana Traven, Thomas Naderer – PLOS Pathogens

“The Restaurant at the End of the Infection — Macrophages as Host Cells”
“So Long and Thanks for All the Inflammatory Cell Death”

Dr. Bik’s Picks

crowSmarter than a first-grader? Crows can perform as well as 7- to 10-year-olds on cause-and-effect water displacement tasks

“New research conducted by UC Santa Barbara’s Corina Logan, with her collaborators at the University of Auckland in New Zealand, demonstrates the birds’ intellectual prowess may be more fact than fiction.”

JBC Journal of Biological ChemistryFour billion-year-old chemistry in cells today – Phys.org

“Parts of the primordial soup in which life arose have been maintained in our cells today according to scientists at the University of East Anglia.”

Screen Shot 2014-07-25 at 9.47.50 PMDustup Over Lionfish Science Fair Project – Bob Grant – The Scientist

A former graduate student says he feels slighted by a failure to attribute his contributions to a line of research regarding the salinity tolerances of an invasive species. “I’m not sure what happened, but my main issue is that the national media has presented a story that is sensationalized, and has left me out of the picture.”

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Microbiome digest, July 24

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Introducing the crAssphage, an 84 bp BLAST from the past, archaea in the Savannah, metabolomics of racehorse microbiome, and X-raying headphones.

Human oral microbiome

Proceedings RoyalMolecular analysis of ancient caries – Marc Simón – Proceedings of the Royal Society, Biological Sciences

“An 84 base pair sequence of the Streptococcus mutans virulence factor, known as dextranase, has been obtained from 10 individuals from the Bronze Age to the Modern Era in Europe and from before and after the colonization in America. “

Human gut microbiome

Nature CommunicationsA highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes – Bas E. Dutilh – Nature Communications

“Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which we refer to as crAssphage.”

Gut family SchlossThe dynamics of a family’s gut microbiota reveal variations on a theme – Patrick D Schloss – Microbiome

“Using 16S rRNA gene and metagenomic shotgun sequence data, it was possible to distinguish the family from a cohort of normal individuals living in the same geographic region and to differentiate each family member”

Pregnancy and Birth

Screen Shot 2014-07-24 at 05.53PM, Jul 24An unnecessary cut? – Sky Dylan-Robbins – The New Yorker

“The most common operating-room procedure in the United States is the Cesarean section. “

Animal microbiome

Equine Vet JournalCharacterisation of the faecal metabolome and microbiome of Thoroughbred racehorses – C. J. Proudman – Equine Veterinary Journal

“Faecal metabolome was characterised using thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS), with spectral analysis performed using AMDIS and compared against the NIST database. Taxonomic description of the faecal microbiota was achieved using error-corrected 454 pyrosequencing data from 16S rRNA gene amplicons”

Journal of MicrobiologyPyrosequencing-based analysis of fecal microbial communities in three purebred pig lines – Edward Alain B. Pajarillo – Journal of Microbiology

“Taxon-dependent and -independent analyses were performed to evaluate differences in the fecal bacterial communities and to identify bacterial genera that can be used to discriminate breeds, following high-throughput pyrosequencing of 16S rRNA genes. “

Environmental microbiome

Screen Shot 2014-07-24 at 05.55PM, Jul 24Seasonal Effects in a Lake Sediment Archaeal Community of the Brazilian Savanna – Thiago Rodrigues – Archaea

“Here we describe for the first time the diversity of archaeal communities from freshwater lake sediments of the Cerrado in the dry season and in the transition period between the dry and rainy seasons, when the first rains occur. Gene libraries were constructed, using Archaea-specific primers for the 16S rRNA and amoA genes.”

Screen Shot 2014-07-24 at 05.56PM, Jul 24Spatial patterns and links between microbial community composition and function in cyanobacterial mats – Mohammad A. Al-Najjar – Frontiers in Microbiology

“Similar clustering was found when the community composition of the mats’ cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis, indicating a significant link between the microbial community composition and function. “

MicrobeNetNew Joint Initiative from the Knight and Sogin Labs as a Follow-up to the MoBEDAC Initiative – Embriette Hyde

“By the end of the funded period, standard 16S rRNA and ITS (fungal) analysis pipelines will be developed and made available to the MoBe community, 16S rRNA and ITS databases will be markedly improved, QIIME and VAMPS will be tightly integrated into a new database engine called QiiTA to facilitate analysis by all MoBe researchers, and two major training workshops will be offered. “

Dr. Bik’s PicksDNA

DNA mostly ‘junk?’ Only 8.2 percent of human DNA is ‘functional’, study finds – Science Daily

“This figure is very different from one given in 2012, when some scientists involved in the ENCODE (Encyclopedia of DNA Elements) project stated that 80% of our genome has some biochemical function.”

Screen Shot 2014-07-24 at 05.58PM, Jul 24Sex differences in medicine – BeWell – Stanford University

“A man can be diagnosed with the same disease as a woman, and yet the course the disease takes in each could prove very different. And a treatment which works for one gender may prove ineffective for the other. “

corksIs Climate Change Ruining Wine Corks? – Kelly Dickerson – LiveScience

“Many people may only worry about corks when it’s time to pop the Champagne, but some experts are worried about wine cork quality, which has been mysteriously in decline for almost 20 years.“

Headphone x rayDoc X-Rays His Broken Headphones to Fix Them – Bahar Gholipour – LiveScience

“”Closed fracture of a speaker wire within its rubber/plastic sleeve is a rare headphone injury, usually due to a traction trauma,” Skalski wrote in his report of the case.”

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